sRNADiff-class {srnadiff}R Documentation

An S4 class to represent sRNA-Seq data for differential expression.

Description

An S4 class to represent sRNA-Seq data for differential expression.

Slots

annotation

The annotation in GRanges format.

bamFileNames

The name of one read file in BAM format.

bamFiles

The BAM files in a BamFileList.

chromosomes

The names of the chromosomes.

chromosomeSizes

The sizes of the chromosomes.

replicates

The names of the replicates.

conditions

The condition to which each replicate belongs.

coverages

The coverages, a vector of RLE.

lengths

The lengths parts of the coverages.

values

The values parts of the coverages.

design

Experimental design, a DataFrame for DESeq2

regions

A GenomicRanges of the possibly differentially expressed region

minDepth

Minimum depth to consider to find regions

minSize

Minimum region size

maxSize

Maximum region size

mergeDistance

Distance to merge consecutive region

minDifferences

Minimum number of different nt between two regions

noDiffToDiff

Transition probability

diffToNoDiff

Transition probability

emission

Emission probability

emissionThreshold

Emission threshold

skipAnnotation

Whether to skip the annotation strategy step

skipNaive

Whether to skip the naive strategy step

skipHmm

Whether to skip the HMM strategy step

skipSlice

Whether to skip the slice strategy step

nThreads

Number of threads


[Package srnadiff version 1.4.0 Index]